bump ALL gatk4 modules

[matthdsm]

• Bump GATK to v 4.6.1.0
• Fix environment files
• Add renovate comments
• Move to wave containers
• Add missing nf-tests
• Fix broken tests
• drop legacy test_data path
• ...

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[maxulysse]

Looking good, but failing tests 😭

[maxulysse]

You sure about the process_single label?

[matthdsm]

Yeah, I was looking at the cpu usage of our cluster and saw gatk using no more than one cpu at the time... I had a reservation of 80 cores of which only 8 were actively doing something....

[matthdsm]

Anything with significant compression/decompression should have process_low

[matthdsm]

If you don't trust it, feel free to revert the commit, we can always patch the modules in our pipelines

[nvnieuwk]

Tests are passing locally and on gitpod, I got approval from Maxime to cowboy merge this in.

@edmundmiller do you think these CI issues can be fixed easily?

[edmundmiller]

This is one of the instances where if the tests pass locally, we should ignore CI and not worry about getting it perfect. It's a guardrail but sometimes we can hop over it.

[matthdsm]

Thank you for the faith @edmundmiller